Genome-wide association studies reveal genomic windows and candidate genes related to fat deposition in chickens.

2016

Predictive ability of Genomic Estimated Family Values (GEFV).

Genomic selection (GS) has been used to compute genomic estimated breeding values (GEBV) of individuals; however, it has only been applied to animal and major plant crops due to high costs. Besides, breeding and selection is performed at the family level in some crops. We aimed to study the implementation of genome-wide family selection (GWFS) in two loblolly pine (Pinus taeda L.) populations: i) the breeding population CCLONES composed of 63 families (5-20 individuals per family), phenotyped for four traits (stem diameter, stem rust susceptibility, tree stiffness and lignin content) and genotyped using an Illumina Infinium assay with 4740 polymorphic SNPs, and ii) a simulated population that reproduced the same pedigree as CCLONES, 5000 polymorphic loci and two traits (oligogenic and polygenic). In both populations, phenotypic and genotypic data was pooled at the family level in silico. Phenotypes were averaged across replicates for all the individuals and allele frequency was computed for each SNP. Marker effects were estimated at the individual (GEBV) and family (GEFV) levels with Bayes-B using the package BGLR in R and models were validated using 10-fold cross validations. Predicted ability, computed by correlating phenotypes with GEBV and GEFV, was always higher for GEFV in both populations, even after standardizing GEFV predictions to be comparable to GEBV. Results revealed great potential for using GWFS in breeding programs that select families, such as most outbreeding forage species. A significant drop in genotyping costs as one sample per family is needed would allow the application of GWFS in minor crops.

Genomic structure and marker-derived gene networks for growth and meat quality traits of brazilian nelore beef cattle.

Nelore is the major beef cattle breed in Brazil with more than 130 million heads. Genome-wide association studies (GWAS) are often used to associate markers and genomic regions to growth and meat quality traits that can be used to assist selection programs. An alternative methodology to traditional GWAS that involves the construction of gene network interactions, derived from results of several GWAS is the AWM (Association Weight Matrices)/PCIT (Partial Correlation and Information Theory). With the aim of evaluating the genetic architecture of Brazilian Nelore cattle, we used high-density SNP genotyping data (~770,000 SNP) from 780 Nelore animals comprising 34 half-sibling families derived from highly disseminated and unrelated sires from across Brazil. The AWM/PCIT methodology was employed to evaluate the genes that participate in a series of eight phenotypes related to growth and meat quality obtained from this Nelore sample.

Polimorfismos nos genes IL-2, IL-5, IL-8, IL-12 e IFN-y e a resposta a nematoides gastrintestinais em caprinos.

Resumo: Cinco genes candidatos foram selecionados para identificar polimorfismos de nucleotídeo único e sua associação com a resposta de caprinos a nematoides gastrintestinais. Para isso, o DNA genômico dos animais mais resistentes e mais susceptíveis foi extraído e submetido ao sequenciamento de nova geração. Foram observados 71 SNPs, sendo 4 associados à resistência, o que os tornam alvos de estudos em toda a população de caprinos a fim de se confirmar essa associação. [Polymorphisms in IL-2, IL-5, IL-8, IL-12 e IFN-y genes and the response to gastrointestinal nematode in goats]. Abstract: Five candidate genes were selected to identify single nucleotide polymorphisms and its association with goat response to gastrointestinal nematodes. Genomic DNA from resistant and susceptible animals was extracted and submitted to new generation sequencing. It was observed 71 SNPs with 4 associated with resistance, which make them targets for studies on the entire population goats in order to confirm this association.